So, after adding 10-20 mods and deleting/merging some others, I decided to use Mlox to sort the mods - after fixing some compatibility problems I loaded Morrowind and, much to my surprise, the initial loading took FAR longer than it used to before re-sorting the plugins with mlox.
This is the current load order:
GameFile0=Bloodmoon Landscape Overhaul 1.0.esmGameFile1=Bloodmoon.esmGameFile2=Book Rotate.esmGameFile3=CastleWars.esmGameFile4=GDR_MasterFile.esmGameFile5=H.E.L.L.U.V.A._Merchant_Containers.esmGameFile6=Havish.esmGameFile7=Kalendaar_V1 - Eng.esmGameFile8=MCA.esmGameFile9=Morrowind Patch 1.6.5 Beta (BTB Edit).esmGameFile10=Morrowind.esmGameFile11=Pegas Horse Ranch v3.1.esmGameFile12=SG-MW-ecology-BM.esmGameFile13=TR_Data.esmGameFile14=TR_Map1.esmGameFile15=Texture Fix 1.8.esmGameFile16=Tribunal.esmGameFile17=A Bard's life - Spellsongs.espGameFile18=A Bard's life - basic.espGameFile19=ACE_Subtitles.espGameFile20=AK_PCClothier_Balmora.espGameFile21=Aduls_Advanced_Combat_Base.espGameFile22=Aduls_Advanced_Combat_Injury_Effects.espGameFile23=Aduls_Advanced_Combat_Paths.espGameFile24=Advanced Herbalism - TR & BM.espGameFile25=Advanced Lockpicking Beta.espGameFile26=Advanced Persuasion.espGameFile27=Ald Redaynia Extended.espGameFile28=Ald_Ruhn_TG_Devil_Tanto_Tweak.espGameFile29=Animated Morrowind 1.0.espGameFile30=Animated Morrowind II.espGameFile31=Animated_Morrowind - Expanded.espGameFile32=Annastia V3.3.espGameFile33=Antares' Big Mod 5 - MCA 6 - patch.espGameFile34=Antares' Big Mod 5.espGameFile35=Antares' Tribunal Main Quest.espGameFile36=BB Dark Brotherhood by Westly.espGameFile37=BB_Clothiers_of_Vvardenfell_v1.1.espGameFile38=BTB - Alchemy.espGameFile39=BTB - Equipment.espGameFile40=BTB - Settings.espGameFile41=BTB - Spells.espGameFile42=Balmora Expansion v1.4.espGameFile43=Balmora Un-Mod.espGameFile44=Better Bodies.espGameFile45=Better Clothes Complete (BTB Edit).espGameFile46=Better Telekinesis.espGameFile47=BetterMusicSystem_v1.1.1.espGameFile48=BigMod2 v2.0 RELEASE.espGameFile49=Blasphemous Revenants.espGameFile50=Blood Lines I_BloodMoon.espGameFile51=Boe_lich_particle.espGameFile52=Bounty Hunters 1.1.espGameFile53=CM_Partners_3.0.espGameFile54=Camonna Tong's violence 1.2.espGameFile55=CastleWars - Updates.ESPGameFile56=Chariots.espGameFile57=Clean Better Caldera.espGameFile58=Clean Ebonheart Interior Expansion.espGameFile59=Clean Fall Damage.espGameFile60=Clean Morrowind_Bandits_Unlocked.espGameFile61=Clean Morrowind_Cities_Unlocked.espGameFile62=Clean Role-Playing Classes, Stealthy Pack.espGameFile63=Clean THFFTribBM_FINAL.espGameFile64=Clean Tales of Seyda Neen.espGameFile65=Clean To Serve Sithis_.espGameFile66=Clean Ultimate Morrowind Anti-Mod.espGameFile67=Clean Welcome to the Arena!.ESPGameFile68=Clean_AK_PCSmithy_v1.0.espGameFile69=Combat Moves.espGameFile70=DB_Attack_Mod3.espGameFile71=DN-GDRv1.espGameFile72=DNGDR-GHD Patch.espGameFile73=DN_1st_Person_Armor.espGameFile74=DN_1st_Person_bodies.espGameFile75=DW_assassination.espGameFile76=Daedric Sorcery.espGameFile77=DagonFel_Well.espGameFile78=Deus Ex Machina - A Steampunkyish Mod.ESPGameFile79=Dirty Deeds.espGameFile80=Disturb_the_dead.espGameFile81=Djangos Dialogue.ESPGameFile82=Dodge Mod 1.2-WD (Enhanced-LD) (Tribunal).espGameFile83=Dread.espGameFile84=Dulsya Isle.espGameFile85=Dwemer_Cyborgs.espGameFile86=EcoAdjCrime (Tresspass Edit).espGameFile87=EcoAdjDaedricDrops.espGameFile88=EcoAdjMerchantSkills (Disposition Edit).espGameFile89=EcoAdjMisc.espGameFile90=Enhanced Detection.espGameFile91=Enhanced Summoning.espGameFile92=Entertainers_Expanded.espGameFile93=Farmer Mod v4.0 NSE.espGameFile94=FightersGuildReanimation.espGameFile95=Fliggerty's Almanac.espGameFile96=Fliggerty's Fleeing Fetchers.espGameFile97=GCD TEO compatibility patch.espGameFile98=GCD_BigMod2_patch.espGameFile99=GCD_SS_patch.espGameFile100=Galsiahs Character Development.espGameFile101=Get_Diseases_1_00.espGameFile102=Go To Jail 3.5 - T B.espGameFile103=Great House Dagoth.espGameFile104=H.E.L.L.U.V.A. Bountiful Books.espGameFile105=H.E.L.L.U.V.A. Complete Weapons.espGameFile106=H.E.L.L.U.V.A._A.A._LIGHT 1.0.espGameFile107=Havish - Reduced Interest Rates.ESPGameFile108=Havish Mini Patch.espGameFile109=Hold it - replacer.espGameFile110=Hold it - resource.espGameFile111=Illuminated Order v1.0 - Bloodmoon Compatibility Extras.espGameFile112=Illuminated Order v1.0.espGameFile113=Immersive Chargen.espGameFile114=Imperial Employment Office.espGameFile115=Import Business the Merchant of Vvardenfell.espGameFile116=Improved Bartering.espGameFile117=Improved Hand to Hand.espGameFile118=Improved Lockpicking.espGameFile119=Improved Open Spell Balance-LD.espGameFile120=Improved Trap Settings (Tribunal).espGameFile121=Juniper's Twin Lamps (1.1 Tribunal).espGameFile122=KS_Julan_Ashlander Companion_1.3.espGameFile123=KS_Stormrider.espGameFile124=Key Replacer Trib & BM.espGameFile125=Khuul Expanded.espGameFile126=Knock Knock Mod 1.2.espGameFile127=LGNPC_AldVelothi_v1_20.espGameFile128=LGNPC_Aldruhn_v1_20.espGameFile129=LGNPC_Aldruhn_v1_20_suppl.espGameFile130=LGNPC_GnaarMok_v1_20.espGameFile131=LGNPC_HlaOad_v1_32.espGameFile132=LGNPC_IndarysManor_v1_51.espGameFile133=LGNPC_Indarys_Manor_v1_45.espGameFile134=LGNPC_Khuul_v2_20.espGameFile135=LGNPC_MaarGan_v1_20.espGameFile136=LGNPC_NoLore_v0_83.espGameFile137=LGNPC_PaxRedoran_v1_20.espGameFile138=LGNPC_Pelagiad_v1_30.espGameFile139=LGNPC_SecretMasters_v1_30.espGameFile140=LGNPC_SoulSicknessPatch_v1_00.espGameFile141=LGNPC_TelMora_v1_20.espGameFile142=LGNPC_TelUvirith_v1_20.espGameFile143=LGNPC_VivecFQ_v2_10.espGameFile144=LGNPC_VivecRedoran_v1_50.espGameFile145=LeFemmArmor.espGameFile146=Less_Generic_Bloodmoon.espGameFile147=Less_Generic_Nerevarine.espGameFile148=Less_Generic_Tribunal.espGameFile149=Leyawiin 1pt1.espGameFile150=Lgnpc_SN.espGameFile151=Lilarcor_v4-1.espGameFile152=Living Statues of Malacath.espGameFile153=Lothavor's Legacy.espGameFile154=MWE_Base.espGameFile155=MWE_Combat.espGameFile156=MWE_MagickaSpells.espGameFile157=Mashed Lists.espGameFile158=Morrowind Crafting 2-1.espGameFile159=Morrowind Crafting Equipment.espGameFile160=NEDE v1.2.espGameFile161=NPC Functionality.espGameFile162=NPC LCV Locks.espGameFile163=NPC LCV Schedules 03.espGameFile164=Nasty Camonna Tong.espGameFile165=Necromancy Realism.espGameFile166=New Argonian Bodies - Mature.espGameFile167=New Khajiit Bodies - Mature.espGameFile168=New Suran Extended 1.5.espGameFile169=NighttimeDoorLocks-LD 1.1a.espGameFile170=No Trespassing ALL.ESPGameFile171=Norn Full.espGameFile172=OJAI - Framerate Version.espGameFile173=Oluhan V1.13.espGameFile174=P.R.E. v4.0 + Nudiy Greeting Expansion.ESPGameFile175=Piratelords Trade Enhancements.espGameFile176=Protective Guards.espGameFile177=Pursuit Enhanced.espGameFile178=RAKFaction0point75.ESPGameFile179=Realistic Combat.espGameFile180=Rectified Fines.ESPGameFile181=Rise of the Illuminated Lich.espGameFile182=SG-MW-ecology-BM-plugin.espGameFile183=SOLcodebook.espGameFile184=SW_LivingCitiesofVvardenfell03-13Patch.espGameFile185=SakakiManor.espGameFile186=Scripted_Spells.espGameFile187=Seekers Faction v2.0.espGameFile188=Service_Requirements+WGI.espGameFile189=Seyda Neen Docks and Haldershore Tribunal_Bloodmoon V1.1.espGameFile190=Sim-ManorAlpha.espGameFile191=Skooma Anonymous.espGameFile192=Sleepers, Awake!.espGameFile193=SoT_Order of Ascadia_V2.1.espGameFile194=South Wall.ESPGameFile195=Spect Sorcery pt 1.espGameFile196=Stealth Enhancements-LD 1.5b (Tribunal).espGameFile197=Suran_Underworld_2.5.espGameFile198=Swimming Realism.espGameFile199=TC_SadrithMoraClosed.espGameFile200=TLM - Complete.espGameFile201=Tales of Tel Branora.espGameFile202=TavernTime Vardenfell.ESPGameFile203=The Broken Drum 1.01.espGameFile204=The Holiday Mod.espGameFile205=The Latest, Greatest Housing Mod_GOLD.espGameFile206=The Sable Dragon 1.5.espGameFile207=The Tribe Unmourned (GHD).espGameFile208=The_Vvardenfell_Libraries.espGameFile209=Thief's Disguise Kit.espGameFile210=Thief's Mask 1.2.espGameFile211=To The Death.espGameFile212=TravelingMerchants_v2.2.espGameFile213=Undeads arise from death 1.4 - T - B.espGameFile214=UnexpurgatedBarenziahv100.espGameFile215=Unique Banners and Signs.espGameFile216=Unleveled Creatures 2.0.espGameFile217=Vampire Realism II - BL Patch.espGameFile218=Vampire Realism II - BM Add-On.espGameFile219=Vampire Realism II - TB Add-On.espGameFile220=Vampire Realism II - VE Patch.espGameFile221=Vampire Realism II.espGameFile222=Vampire_Embrace.espGameFile223=Vivec Expansion 2.0.espGameFile224=Vivec's Fate.espGameFile225=Voice Addons.ESPGameFile226=Vurt's Ashlands Overhaul.espGameFile227=Vurt's Grazelands Trees.espGameFile228=Vurt's Solstheim Trees & Bushes Replacer.espGameFile229=Vvardenfell Druglord.espGameFile230=Wanderers of Solstheim.espGameFile231=War_Against_the_Dark_Brotherhood.espGameFile232=Wayfarer's Rest v1.21.espGameFile233=Weather Effects.espGameFile234=WeatheredSigns.espGameFile235=Westly's Master Headpack X.espGameFile236=Westly_Presents_Unique_Corprus_Stalkers.espGameFile237=What Thieves Guild.ESPGameFile238=Xenn's Strict Factions.ESPGameFile239=abotGuars.espGameFile240=beware of pickpockets! 1.4.espGameFile241=blackjack.espGameFile242=chemwar.espGameFile243=constance1_0.espGameFile244=construction v1.02.espGameFile245=dh_furn.espGameFile246=dh_furn_stores.espGameFile247=dracandrosvoice.espGameFile248=horationpcenhanced12-ve.espGameFile249=sm_luckylockupadditions.espGameFile250=vgreetings-combined.ESP